Quantification of rolling circle amplified DNA using magnetic nanobeads and a Blu-ray optical pick-up unit

Abstract: We present the first implementation of a Blu-ray optical pickup unit (OPU) for the high-performance low-cost readout of a homogeneous assay in a multi-chamber microfluidic disc with a chamber thickness of 600 μm. The assay relies on optical measurements of the dynamics of magnetic nanobeads in an
oscillating magnetic field applied along the light propagation direction. The laser light provided by the
OPU is transmitted through the sample chamber and reflected back onto the photodetector array of the
OPU via a mirror. Spectra of the 2nd harmonic photodetector signal vs. the frequency of the applied
magnetic field show a characteristic peak due to freely rotating magnetic nanobeads. Beads bound to
1 μm coils of DNA formed off-chip by padlock probe recognition and rolling circle amplification show a
different dynamics and the intensity of the characteristic peak decreases. We have determined the
optimum magnetic bead concentration to 0.1 mg/mL and have measured the response vs. concentration
of DNA coils formed from Escherichia Coli. We have found a limit of detection of 10 pM and a dynamic
range of about two orders of magnitude, which is comparable to the performance obtained using costly
and bulky laboratory equipment. The presented device leverages on the advanced but low-cost
the technology of Blu-ray OPUs to provide a low-cost and high-performance magnetic bead-based readout
of homogeneous bioassays. The device is highly flexible and we have demonstrated its use on microfluidic
chambers in a disc with a thickness compatible with current optical media mass-production facilities.

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